Merge branch 'develop' into imp/JAL-2775

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 3ba9947..31c20ed 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -83,18 +83,18 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * list of sequenceSet ids associated with the view
    */
-  protected List<String> _aps = new ArrayList<String>();
+  protected List<String> _aps = new ArrayList<>();
 
   /**
    * list of alignment panels to use for superposition
    */
-  protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+  protected Vector<AlignmentPanel> _alignwith = new Vector<>();
 
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
-  protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+  protected Vector<AlignmentPanel> _colourwith = new Vector<>();
 
   private String viewId = null;
 
@@ -170,7 +170,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     if (_alignwith == null)
     {
-      _alignwith = new Vector<AlignmentPanel>();
+      _alignwith = new Vector<>();
     }
     if (_alignwith.size() == 0 && ap != null)
     {
@@ -310,6 +310,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public abstract ViewerType getViewerType();
 
+  protected abstract IProgressIndicator getIProgressIndicator();
+
   /**
    * add a new structure (with associated sequences and chains) to this viewer,
    * retrieving it if necessary first.
@@ -460,7 +462,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * create the mappings
      */
     apanel.getStructureSelectionManager().setMapping(seq, chains,
-            pdbFilename, DataSourceType.FILE);
+            pdbFilename, DataSourceType.FILE, getIProgressIndicator());
 
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features
@@ -468,7 +470,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     if (apanel.getSeqPanel().seqCanvas.fr != null)
     {
       apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
-      apanel.paintAlignment(true);
+      // note - we don't do a refresh for structure here because we do it
+      // explicitly for all panels later on
+      apanel.paintAlignment(true, false);
     }
 
     /*
@@ -717,11 +721,11 @@ public abstract class StructureViewerBase extends GStructureViewer
 
     if (_colourwith == null)
     {
-      _colourwith = new Vector<AlignmentPanel>();
+      _colourwith = new Vector<>();
     }
     if (_alignwith == null)
     {
-      _alignwith = new Vector<AlignmentPanel>();
+      _alignwith = new Vector<>();
     }
 
     ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
@@ -888,7 +892,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     binding.setColourBySequence(seqColour.isSelected());
     if (_colourwith == null)
     {
-      _colourwith = new Vector<AlignmentPanel>();
+      _colourwith = new Vector<>();
     }
     if (binding.isColourBySequence())
     {